Academic Journal
Comparative Genomic Hybridization (CGH) in Genotoxicology: From the Basics to Modern Approaches.
| Τίτλος: | Comparative Genomic Hybridization (CGH) in Genotoxicology: From the Basics to Modern Approaches. |
|---|---|
| Συγγραφείς: | Nisar N; York St John University, School of Health Sciences, Biomedical Science, Lord Mayor's Walk, York, UK., Baumgartner A; York St John University, School of Health Sciences, Biomedical Science, Lord Mayor's Walk, York, UK. a.baumgartner@yorksj.ac.uk. |
| Πηγή: | Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2026; Vol. 2986, pp. 247-277. |
| Τύπος έκδοσης: | Journal Article; Review |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE |
| Imprint Name(s): | Publication: Totowa, NJ : Humana Press Original Publication: Clifton, N.J. : Humana Press |
| Ιατρικοί όροι (MeSH): | Comparative Genomic Hybridization*/methods , Toxicogenetics*/methods, High-Throughput Nucleotide Sequencing/methods ; Mutagenicity Tests/methods ; Genomics/methods ; Gene Editing/methods ; Humans ; DNA Copy Number Variations ; Machine Learning ; Animals |
| Περίληψη: | Over the past two decades, comparative genomic hybridization (CGH) and array CGH have become essential tools in clinical diagnostics, oncology, and toxicological risk assessment. Initially developed to identify chromosomal imbalances like copy number variations (CNVs) in tumor cells, these technologies have expanded into genotoxicology and toxicogenomics, exploring gene responses to toxic agents and their molecular mechanisms. As of 2024, new developments include integrating array CGH with next-generation sequencing (NGS), machine learning, and CRISPR-Cas9 genome editing, greatly improving precision. High-density CGH arrays now offer single-cell resolution, enabling the detection of cellular heterogeneity in toxic responses, while long-read sequencing facilitates the identification of complex genomic rearrangements. Recent innovations include combining CGH and toxicogenomics with organ-on-chip models for real-time, tissue-specific toxicological assessment. This has significantly improved the relevance of toxicological data for human health. However, while these advances are promising, array CGH remains costly and requires substantial data processing, driving the need for advanced bioinformatics tools. AI-driven predictive toxicology models are also gaining traction, correlating toxicogenomic profiles with clinical outcomes. Despite these advancements, the field still faces challenges, such as evolving regulatory guidelines and complex data interpretation, which hinder broader adoption and the full realization of CGH's potential in toxicology and risk assessment. (© 2026. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.) |
| References: | Pinkel D, Straume T, Gray JW (1986) Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci USA 83(9):2934–2938. (PMID: 345825432342110.1073/pnas.83.9.2934) Laan M, Kallioniemi OP, Hellsten E et al (1995) Mechanically stretched chromosomes as targets for high-resolution FISH mapping. Genome Res 5(1):13–20. (PMID: 871705110.1101/gr.5.1.13) Pang AW, MacDonald JR, Pinto D et al (2010) Towards a comprehensive structural variation map of an individual human genome. Genome Biol 11(5):R52. (PMID: 20482838289806510.1186/gb-2010-11-5-r52) Raap AK, Tanke HJ (2006) COmbined Binary RAtio fluorescence in situ hybridiziation (COBRA-FISH): development and applications. Cytogenet Genome Res 114(3–4):222–226. (PMID: 1695465710.1159/000094204) Heng HH, Squire J, Tsui LC (1992) High-resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc Natl Acad Sci USA 89(20):9509–9513. (PMID: 13840555016110.1073/pnas.89.20.9509) Schrock E, du Manoir S, Veldman T et al (1996) Multicolor spectral karyotyping of human chromosomes. Science 273(5274):494–497. (PMID: 866253710.1126/science.273.5274.494) Speicher MR, Gwyn Ballard S, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12(4):368–375. (PMID: 863048910.1038/ng0496-368) Bolzer A, Kreth G, Solovei I et al (2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3(5):e157. (PMID: 15839726108433510.1371/journal.pbio.0030157) Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2(4):292–301. (PMID: 1128370110.1038/35066075) Chen B, Gilbert LA, Cimini BA et al (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155(7):1479–1491. (PMID: 24360272391850210.1016/j.cell.2013.12.001) Deng W, Shi X, Tjian R et al (2015) CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. Proc Natl Acad Sci USA 112(38):11870–11875. (PMID: 26324940458683710.1073/pnas.1515692112) Huang Y, Fernandez SV, Goodwin S et al (2007) Epithelial to mesenchymal transition in human breast epithelial cells transformed by 17beta-estradiol. Cancer Res 67(23):11147–11157. (PMID: 1805643910.1158/0008-5472.CAN-07-1371) Kallioniemi A, Kallioniemi OP, Sudar D et al (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258(5083):818–821. (PMID: 135964110.1126/science.1359641) Pinkel D, Segraves R, Sudar D et al (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20(2):207–211. (PMID: 977171810.1038/2524) Albertini RJ, Anderson D, Douglas GR et al (2000) IPCS guidelines for the monitoring of genotoxic effects of carcinogens in humans. International Programme on Chemical Safety. Mutat Res 463(2):111–172. (PMID: 1091390810.1016/S1383-5742(00)00049-1) Zhao EY, Jones M, Jones SJM (2019) Whole-genome sequencing in cancer. Cold Spring Harb Perspect Med 9(3):a034579. (PMID: 29844223639634310.1101/cshperspect.a034579) van Delft J, Gaj S, Lienhard M et al (2012) RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene. Toxicol Sci 130(2):427–439. (PMID: 2288981110.1093/toxsci/kfs250) Kreuzer K, Sprenger H, Braeuning A (2022) Comparative analysis of transcriptional responses to genotoxic and non-genotoxic agents in the blood cell model TK6 and the liver model HepaRG. Int J Mol Sci 23(7):3420. (PMID: 35408779899874510.3390/ijms23073420) Afshari CA, Hamadeh HK, Bushel PR (2011) The evolution of bioinformatics in toxicology: advancing toxicogenomics. Toxicol Sci 120(Suppl 1):S225–S237. (PMID: 2117777510.1093/toxsci/kfq373) Skardal A (2024) Grand challenges in organoid and organ-on-a-chip technologies. Front Bioeng Biotechnol 12:1366280. (PMID: 384560041091939910.3389/fbioe.2024.1366280) Zhao Y, Lann S, Okhovatian S et al (2024) Integrating organoids and organ-on-a-chip devices. Nat Rev Bioeng 2:588–608. (PMID: 10.1038/s44222-024-00207-z) Maqsood K, Hagras H, Radu Zabet N (2024) An overview of artifcial intelligence in the feld of genomics. Discov Artif Intell 4:9. (PMID: 10.1007/s44163-024-00103-w) Pinkel D, Albertson DG (2005) Comparative genomic hybridization. Annu Rev Genomics Hum Genet 6:331–354. (PMID: 1612486510.1146/annurev.genom.6.080604.162140) Schmeisser S, Miccoli A, von Bergen M et al (2023) New approach methodologies in human regulatory toxicology – not if, but how and when! Environ Int 178:108082. (PMID: 374229751085868310.1016/j.envint.2023.108082) du Manoir S, Speicher MR, Joos S et al (1993) Detection of complete and partial chromosome gains and losses by comparative genomic in situ hybridization. Hum Genet 90(6):590–610. (PMID: 844446510.1007/BF00202476) Redon R, Carter NP (2009) Comparative genomic hybridization: microarray design and data interpretation. Methods Mol Biol 529:37–49. (PMID: 19381971287131010.1007/978-1-59745-538-1_3) Aradhya S, Cherry AM (2007) Array-based comparative genomic hybridization: clinical contexts for targeted and whole-genome designs. Genet Med 9(9):553–559. (PMID: 1787364210.1097/GIM.0b013e318149e354) Carreira IM, Ferreira SI, Matoso E et al (2015) Copy number variants prioritization after array-CGH analysis – a cohort of 1000 patients. Mol Cytogenet 8:103. (PMID: 26719768469624710.1186/s13039-015-0202-z) Wa CV, DeVries S, Chen YY et al (2005) Clinical application of array-based comparative genomic hybridization to define the relationship between multiple synchronous tumors. Mod Pathol 18(4):591–597. (PMID: 1569612910.1038/modpathol.3800332) Pinkel D, Albertson DG (2005) Array comparative genomic hybridization and its applications in cancer. Nat Genet 37(Suppl):S11–S17. (PMID: 1592052410.1038/ng1569) Albertson DG, Ylstra B, Segraves R et al (2000) Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet 25(2):144–146. (PMID: 1083562610.1038/75985) Han W, Jung EM, Cho J et al (2008) DNA copy number alterations and expression of relevant genes in triple-negative breast cancer. Genes Chromosomes Cancer 47(6):490–499. (PMID: 1831490810.1002/gcc.20550) Snijders AM, Nowak N, Segraves R et al (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29(3):263–264. (PMID: 1168779510.1038/ng754) Baslan T, Kendall J, Rodgers L et al (2012) Genome-wide copy number analysis of single cells. Nat Protoc 7(6):1024–1041. (PMID: 22555242506970110.1038/nprot.2012.039) Masset H, Ding J, Dimitriadou E et al (2022) Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing. Nucleic Acids Res 50(11):e63. (PMID: 35212381922649510.1093/nar/gkac134) Carter NP (2007) Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 39(7 Suppl):S16–S21. (PMID: 17597776269749410.1038/ng2028) Schoumans J, Nielsen K, Jeppesen I et al (2004) A comparison of different metaphase CGH methods for the detection of cryptic chromosome aberrations of defined size. Eur J Hum Genet 12(6):447–454. (PMID: 1502678410.1038/sj.ejhg.5201175) Tachdjian G, Aboura A, Lapierre JM et al (2000) Cytogenetic analysis from DNA by comparative genomic hybridization. Ann Genet 43(3–4):147–154. (PMID: 1116419710.1016/S0003-3995(00)01028-5) Kallioniemi OP, Kallioniemi A, Sudar D et al (1993) Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin Cancer Biol 4(1):41–46. (PMID: 8448377) Piper J, Rutovitz D, Sudar D et al (1995) Computer image analysis of comparative genomic hybridization. Cytometry 19(1):10–26. (PMID: 770518110.1002/cyto.990190104) Zitzelsberger H, Lehmann L, Werner M et al (1997) Comparative genomic hybridisation for the analysis of chromosomal imbalances in solid tumours and haematological malignancies. Histochem Cell Biol 108(4–5):403–417. (PMID: 938793310.1007/s004180050181) Martinez-Granero F, Blanco-Kelly F, Sanchez-Jimeno C et al (2021) Comparison of the diagnostic yield of aCGH and genome-wide sequencing across different neurodevelopmental disorders. NPJ Genom Med 6(1):25. (PMID: 33767182799471310.1038/s41525-021-00188-7) Michels E, De Preter K, Van Roy N et al (2007) Detection of DNA copy number alterations in cancer by array comparative genomic hybridization. Genet Med 9(9):574–584. (PMID: 1787364510.1097/GIM.0b013e318145b25b) Shakoori AR (2017) Fluorescence in situ hybridization (FISH) and its applications. In: Bhat TA, Wani AA (eds) Chromosome structure and aberrations. Springer, pp 343–367. (PMID: 10.1007/978-81-322-3673-3_16) Jobanputra V, Kriplani A, Choudhry VP et al (1998) Detection of chromosomal abnormalities using fluorescence in situ hybridization (FISH). Natl Med J India 11(6):259–263. (PMID: 10083791) Lee VC, Chow JF, Lau EY et al (2015) Comparison between fluorescent in-situ hybridisation and array comparative genomic hybridisation in preimplantation genetic diagnosis in translocation carriers. Hong Kong Med J 21(1):16–22. (PMID: 25345996) Sugimura H (2008) Detection of chromosome changes in pathology archives: an application of microwave-assisted fluorescence in situ hybridization to human carcinogenesis studies. Carcinogenesis 29(4):681–687. (PMID: 1828304210.1093/carcin/bgn046) Larramendy ML, El-Rifai W, Knuutila S (1998) Comparison of fluorescein isothiocyanate- and Texas red-conjugated nucleotides for direct labeling in comparative genomic hybridization. Cytometry 31(3):174–179. (PMID: 951571610.1002/(SICI)1097-0320(19980301)31:3<174::AID-CYTO4>3.0.CO;2-L) Berisha SZ, Shetty S, Prior TW et al (2020) Cytogenetic and molecular diagnostic testing associated with prenatal and postnatal birth defects. Birth Defects Res 112(4):293–306. (PMID: 32115903929095410.1002/bdr2.1648) Miller DT, Adam MP, Aradhya S et al (2010) Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 86(5):749–764. (PMID: 20466091286900010.1016/j.ajhg.2010.04.006) Zhao M, Wang Q, Wang Q et al (2013) Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics 14(Suppl 11):S1. (PMID: 24564169384687810.1186/1471-2105-14-S11-S1) Chiang DY, Getz G, Jaffe DB et al (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6(1):99–103. (PMID: 1904341210.1038/nmeth.1276) Stefanicka-Wojtas D, Kurpas D (2023) Personalised medicine-implementation to the healthcare system in Europe (focus group discussions). J Pers Med 13(3):380. (PMID: 369835621005856810.3390/jpm13030380) Shao L, Kang SH, Li J et al (2010) Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics. J Mol Diagn 12(5):670–679. (PMID: 20724749292843210.2353/jmoldx.2010.090192) Lingjaerde OC, Baumbusch LO, Liestol K et al (2005) CGH-explorer: a program for analysis of array-CGH data. Bioinformatics 21(6):821–822. (PMID: 1553161010.1093/bioinformatics/bti113) Solinas-Toldo S, Lampel S, Stilgenbauer S et al (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20(4):399–407. (PMID: 940875710.1002/(SICI)1098-2264(199712)20:4<399::AID-GCC12>3.0.CO;2-I) Chen W, Erdogan F, Ropers HH et al (2005) CGHPRO – a comprehensive data analysis tool for array CGH. BMC Bioinformatics 6:85. (PMID: 15807904127426810.1186/1471-2105-6-85) Fridlyand J, Snijders AM, Pinkel D et al (2004) Hidden Markov models approach to the analysis of array CGH data. J Multivar Anal 90(1):132–153. (PMID: 10.1016/j.jmva.2004.02.008) Liva S, Hupe P, Neuvial P et al (2006) CAPweb: a bioinformatics CGH array analysis platform. Nucleic Acids Res 34(Web Server issue):W477–W481. (PMID: 16845053153885210.1093/nar/gkl215) Riggs ER, Andersen EF, Cherry AM et al (2020) Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med 22(2):245–257. (PMID: 3169083510.1038/s41436-019-0686-8) Komura D, Shen F, Ishikawa S et al (2006) Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res 16(12):1575–1584. (PMID: 17122084166564110.1101/gr.5629106) Jones JA, McMahon NP, Zheng T et al (2021) Oligonucleotide conjugated antibody strategies for cyclic immunostaining. Sci Rep 11(1):23844. (PMID: 34903759866895610.1038/s41598-021-03135-9) Theisen A (2008) Microarray-based comparative genomic hybridization (aCGH). Nat Educ 1(1):45. Harper JC, Harton G (2010) The use of arrays in preimplantation genetic diagnosis and screening. Fertil Steril 94(4):1173–1177. (PMID: 2057964110.1016/j.fertnstert.2010.04.064) Van der Aa N, Zamani Esteki M, Vermeesch JR et al (2013) Preimplantation genetic diagnosis guided by single-cell genomics. Genome Med 5(8):71. (PMID: 23998893397912210.1186/gm475) Tsuiko O, Fernandez Gallardo E, Voet T et al (2020) Preimplantation genetic testing: single-cell technologies at the forefront of PGT and embryo research. Reproduction 160(5):A19–A31. (PMID: 3306554510.1530/REP-20-0102) Bejjani BA, Shaffer LG (2006) Application of array-based comparative genomic hybridization to clinical diagnostics. J Mol Diagn 8(5):528–533. (PMID: 17065418187617610.2353/jmoldx.2006.060029) Levy B, Wapner R (2018) Prenatal diagnosis by chromosomal microarray analysis. Fertil Steril 109(2):201–212. (PMID: 29447663585615410.1016/j.fertnstert.2018.01.005) Herzog CR, Desai D, Amin S (2006) Array CGH analysis reveals chromosomal aberrations in mouse lung adenocarcinomas induced by the human lung carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Biochem Biophys Res Commun 341(3):856–863. (PMID: 1645505610.1016/j.bbrc.2006.01.043) Heinloth AN, Shackelford RE, Innes CL et al (2003) ATM-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and UV irradiation. Radiat Res 160(3):273–290. (PMID: 1292698610.1667/RR3047) Brown N, Finnon R, Manning G et al (2015) Influence of radiation quality on mouse chromosome 2 deletions in radiation-induced acute myeloid leukaemia. Mutat Res Genet Toxicol Environ Mutagen 793:48–54. (PMID: 2652037210.1016/j.mrgentox.2015.07.012) Cooper CS (2001) Applications of microarray technology in breast cancer research. Breast Cancer Res 3(3):158–175. (PMID: 1130595113868110.1186/bcr291) Coughlin CR 2nd, Scharer GH, Shaikh TH (2012) Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns. Genome Med 4(10):80. (PMID: 23114084358044910.1186/gm381) Wang H, Chen L, Li D et al (2017) Microarray analysis of lung long non-coding RNAs in cigarette smoke-exposed mouse model. Oncotarget 8(70):115647–115656. (PMID: 29383188577780010.18632/oncotarget.23362) Szabo RT, Kovacs-Weber M, Balogh KM et al (2024) Effect of aflatoxin B1 and sterigmatocystin on DNA repair genes in common carp. Aquat Toxicol 276:107076. (PMID: 3927799210.1016/j.aquatox.2024.107076) Brennan KM, Oh SY, Yiannikouris A et al (2017) Differential gene expression analysis of bovine macrophages after exposure to the Penicillium mycotoxins citrinin and/or ochratoxin A. Toxins (Basel) 9(11):366. (PMID: 29137202570598110.3390/toxins9110366) Hester SD, Reid L, Nowak N et al (2009) Comparison of comparative genomic hybridization technologies across microarray platforms. J Biomol Tech 20(2):135–151. (PMID: 195036252685605) Baken KA, Vandebriel RJ, Pennings JL et al (2007) Toxicogenomics in the assessment of immunotoxicity. Methods 41(1):132–141. (PMID: 1716131010.1016/j.ymeth.2006.07.010) Milan M, Coppe A, Reinhardt R et al (2011) Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring. BMC Genomics 12:234. (PMID: 21569398310781510.1186/1471-2164-12-234) Shah SP, Xuan X, DeLeeuw RJ et al (2006) Integrating copy number polymorphisms into array CGH analysis using a robust HMM. Bioinformatics 22(14):e431–e439. (PMID: 1687350410.1093/bioinformatics/btl238) Guha S, Li Y, Neuberg D (2008) Bayesian hidden Markov modeling of array CGH data. J Am Stat Assoc 103(482):485–497. (PMID: 22375091328662210.1198/016214507000000923) Vermeesch JR, Melotte C, Froyen G et al (2005) Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis. J Histochem Cytochem 53(3):413–422. (PMID: 1575003110.1369/jhc.4A6436.2005) Shaw-Smith C, Redon R, Rickman L et al (2004) Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 41(4):241–248. (PMID: 15060094173572610.1136/jmg.2003.017731) Brazma A (2009) Minimum information about a microarray experiment (MIAME)-successes, failures, challenges. ScientificWorldJournal 9:420–423. (PMID: 19484163582322410.1100/tsw.2009.57) Brazma A, Hingamp P, Quackenbush J et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29(4):365–371. (PMID: 1172692010.1038/ng1201-365) Liu Y, Li A, Feng H et al (2015) TAFFYS: an integrated tool for comprehensive analysis of genomic aberrations in tumor samples. PLoS One 10(6):e0129835. (PMID: 26111017448239410.1371/journal.pone.0129835) Quigley D (2015) Equalizer reduces SNP bias in Affymetrix microarrays. BMC Bioinformatics 16:238. (PMID: 26223252451888910.1186/s12859-015-0669-y) Mayrhofer M, Viklund B, Isaksson A (2016) Rawcopy: improved copy number analysis with Affymetrix arrays. Sci Rep 6:36158. (PMID: 27796336508694010.1038/srep36158) Morgan AP (2015) argyle: an R package for analysis of illumina genotyping arrays. G3 (Bethesda) 6(2):281–286. (PMID: 26684930475154810.1534/g3.115.023739) Chan VSW, Theilade MD (2005) The use of toxicogenomic data in risk assessment: a regulatory perspective. Clin Toxicol 43(2):121–126. (PMID: 10.1081/CLT-50407) Tice RR, Austin CP, Kavlock RJ et al (2013) Improving the human hazard characterization of chemicals: a Tox21 update. Environ Health Perspect 121(7):756–765. (PMID: 23603828370199210.1289/ehp.1205784) Aardema MJ, MacGregor JT (2002) Toxicology and genetic toxicology in the new era of “toxicogenomics”: impact of “-omics” technologies. Mutat Res 499(1):13–25. (PMID: 11804602) Davis AP, King BL, Mockus S et al (2011) The comparative toxicogenomics database: update 2011. Nucleic Acids Res 39(Database issue):D1067–D1072. (PMID: 2086444810.1093/nar/gkq813) Nuwaysir EF, Bittner M, Trent J et al (1999) Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog 24(3):153–159. (PMID: 1020479910.1002/(SICI)1098-2744(199903)24:3<153::AID-MC1>3.0.CO;2-P) Lettieri T (2006) Recent applications of DNA microarray technology to toxicology and ecotoxicology. Environ Health Perspect 114(1):4–9. (PMID: 16393650133264810.1289/ehp.8194) Gerhold D, Lu MQ, Xu J et al (2001) Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays. Physiol Genomics 5(4):161–170. (PMID: 1132896110.1152/physiolgenomics.2001.5.4.161) OECD (2009) Series on testing and assessment no. 100 – report of the second survey on available omics tools (ENV/JM/MONO(2008)35). Available at http://www.oecd.org/officialdocuments/displaydocument/?cote=env/jm/mono(2008)35&doclanguage=en . Accessed: 22 June 2018. Vrana KE, Freeman WM, Aschner M (2003) Use of microarray technologies in toxicology research. Neurotoxicology 24(3):321–332. (PMID: 1278209810.1016/S0161-813X(02)00193-6) Awuah WA, Shah MH, Sanker V et al (2025) Advances in chromosomal microarray analysis: transforming neurology and neurosurgery. Brain Spine 5:104197. (PMID: 399901161184712610.1016/j.bas.2025.104197) EMBL (2025) Highlights 2024. Available at https://www.embl.org/documents/wp-content/uploads/2025/03/EMBL-EBI-Highlights-Report-2024.pdf . Accessed: 9 June 2025. Bottosso M, Mosele F, Michiels S et al (2024) Moving toward precision medicine to predict drug sensitivity in patients with metastatic breast cancer. ESMO Open 9(3):102247. (PMID: 384012481098286310.1016/j.esmoop.2024.102247) Pereira R, Oliveira J, Sousa M (2020) Bioinformatics and computational tools for next-generation sequencing analysis in clinical genetics. J Clin Med 9(1):132. (PMID: 31947757701934910.3390/jcm9010132) Davis AP, Grondin CJ, Johnson RJ et al (2017) The comparative toxicogenomics database: update 2017. Nucleic Acids Res 45(D1):D972–D978. (PMID: 2765145710.1093/nar/gkw838) Mattingly CJ, Rosenstein MC, Davis AP et al (2006) The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. Toxicol Sci 92(2):587–595. (PMID: 16675512158611110.1093/toxsci/kfl008) Davis AP, Wiegers TC, Wiegers J et al (2018) Chemical-induced phenotypes at CTD help inform the predisease state and construct adverse outcome pathways. Toxicol Sci 165(1):145–156. (PMID: 29846728611178710.1093/toxsci/kfy131) Grondin CJ, Davis AP, Wiegers TC et al (2018) Accessing an expanded exposure science module at the comparative toxicogenomics database. Environ Health Perspect 126(1):014501. (PMID: 29351546601468810.1289/EHP2873) Young RR (2002) Genetic toxicology: web resources. Toxicology 173(1–2):103–121. (PMID: 1195568810.1016/S0300-483X(02)00026-4) Lea IA, Gong H, Paleja A et al (2017) CEBS: a comprehensive annotated database of toxicological data. Nucleic Acids Res 45(D1):D964–D971. (PMID: 2789966010.1093/nar/gkw1077) Andersen ME, Al-Zoughool M, Croteau M et al (2010) The future of toxicity testing. J Toxicol Environ Health B Crit Rev 13(2–4):163–196. (PMID: 2057489610.1080/10937404.2010.483933) Andersen ME, Krewski D (2009) Toxicity testing in the 21st century: bringing the vision to life. Toxicol Sci 107(2):324–330. (PMID: 1907476310.1093/toxsci/kfn255) Andersen ME, Krewski D (2010) The vision of toxicity testing in the 21st century: moving from discussion to action. Toxicol Sci 117(1):17–24. (PMID: 2057378410.1093/toxsci/kfq188) Testing CoT, Assessment of Environmental Agents NRC (2007) Toxicity testing in the 21st century: a vision and a strategy. The National Academies Press, Washington, DC. Hendrickx DM, Boyles RR, Kleinjans JC et al (2014) Workshop report: identifying opportunities for global integration of toxicogenomics databases, 26-27 June 2013, Research Triangle Park, NC, USA. Arch Toxicol 88(12):2323–2332. (PMID: 25326818424747810.1007/s00204-014-1387-3) Jacobs A (2009) An FDA perspective on the nonclinical use of the X-Omics technologies and the safety of new drugs. Toxicol Lett 186(1):32–35. (PMID: 1880947610.1016/j.toxlet.2008.08.013) Bhattacharya S, Zhang Q, Carmichael PL et al (2011) Toxicity testing in the 21 century: defining new risk assessment approaches based on perturbation of intracellular toxicity pathways. PLoS One 6(6):e20887. (PMID: 21701582311880210.1371/journal.pone.0020887) Krewski D, Westphal M, Al-Zoughool M et al (2011) New directions in toxicity testing. Annu Rev Public Health 32:161–178. (PMID: 2121915410.1146/annurev-publhealth-031210-101153) Chepelev NL, Moffat ID, Labib S et al (2015) Integrating toxicogenomics into human health risk assessment: lessons learned from the benzo[a]pyrene case study. Crit Rev Toxicol 45(1):44–52. (PMID: 2560502710.3109/10408444.2014.973935) Moffat I, Chepelev N, Labib S et al (2015) Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water. Crit Rev Toxicol 45(1):1–43. (PMID: 25605026452160810.3109/10408444.2014.973934) Harrill AH, Rusyn I (2008) Systems biology and functional genomics approaches for the identification of cellular responses to drug toxicity. Expert Opin Drug Metab Toxicol 4(11):1379–1389. (PMID: 18950280261428410.1517/17425255.4.11.1379) Zhang Q, Bhattacharya S, Andersen ME et al (2010) Computational systems biology and dose-response modeling in relation to new directions in toxicity testing. J Toxicol Environ Health B Crit Rev 13(2–4):253–276. (PMID: 2057490110.1080/10937404.2010.483943) Grant GR, Manduchi E, Stoeckert CJ Jr (2007) Analysis and management of microarray gene expression data [Chapter 19, unit 6]. Curr Protoc Mol Biol 77(1):1–30. (PMID: 10.1002/0471142727.mb1906s77) Gatzidou ET, Zira AN, Theocharis SE (2007) Toxicogenomics: a pivotal piece in the puzzle of toxicological research. J Appl Toxicol 27(4):302–309. (PMID: 1742980010.1002/jat.1248) Jean-Quartier C, Jeanquartier F, Jurisica I et al (2018) In silico cancer research towards 3R. BMC Cancer 18(1):408. (PMID: 29649981589793310.1186/s12885-018-4302-0) Vachon J, Page-Lariviere F, Sirard MA et al (2018) Availability, quality, and relevance of toxicogenomics data for human health risk assessment: a scoping review of the literature on trihalomethanes. Toxicol Sci 163(2):364–373. (PMID: 2951433210.1093/toxsci/kfy050) Telenius H, Carter NP, Bebb CE et al (1992) Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13(3):718–725. (PMID: 163939910.1016/0888-7543(92)90147-K) Zhang L, Cui X, Schmitt K et al (1992) Whole genome amplification from a single cell: implications for genetic analysis. Proc Natl Acad Sci USA 89(13):5847–5851. (PMID: 16310674939410.1073/pnas.89.13.5847) Huber R, Kulka U, Lorch T et al (2001) Technical report: application of the Metafer2 fluorescence scanning system for the analysis of radiation-induced chromosome aberrations measured by FISH-chromosome painting. Mutat Res 492(1–2):51–57. (PMID: 1137724310.1016/S1383-5718(01)00151-6) Bangs CD, Donlon TA (2005) Metaphase chromosome preparation from cultured peripheral blood cells. Curr Protoc Hum Genet Chapter 4:Unit 4.1. (PMID: 18428376) du Manoir S, Kallioniemi OP, Lichter P et al (1995) Hardware and software requirements for quantitative analysis of comparative genomic hybridization. Cytometry 19(1):4–9. (PMID: 770518310.1002/cyto.990190103) du Manoir S, Schrock E, Bentz M et al (1995) Quantitative analysis of comparative genomic hybridization. Cytometry 19(1):27–41. (PMID: 770518210.1002/cyto.990190105) Lundsteen C, Maahr J, Christensen B et al (1995) Image analysis in comparative genomic hybridization. Cytometry 19(1):42–50. (PMID: 770518410.1002/cyto.990190106) |
| Contributed Indexing: | Keywords: Array CGH; CGH; Comparative genomic hybridization; Genomic imbalances; Genotoxicology; Microarray; Toxicogenomics |
| Entry Date(s): | Date Created: 20251122 Date Completed: 20251122 Latest Revision: 20260424 |
| Update Code: | 20260425 |
| DOI: | 10.1007/978-1-0716-4976-3_12 |
| PMID: | 41273687 |
| Βάση Δεδομένων: | MEDLINE |
| FullText | Text: Availability: 0 |
|---|---|
| Header | DbId: cmedm DbLabel: MEDLINE An: 41273687 AccessLevel: 3 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: Comparative Genomic Hybridization (CGH) in Genotoxicology: From the Basics to Modern Approaches. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AU" term="%22Nisar+N%22">Nisar N</searchLink>; York St John University, School of Health Sciences, Biomedical Science, Lord Mayor's Walk, York, UK.<br /><searchLink fieldCode="AU" term="%22Baumgartner+A%22">Baumgartner A</searchLink>; York St John University, School of Health Sciences, Biomedical Science, Lord Mayor's Walk, York, UK. a.baumgartner@yorksj.ac.uk. – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%229214969%22">Methods in molecular biology (Clifton, N.J.)</searchLink> [Methods Mol Biol] 2026; Vol. 2986, pp. 247-277. – Name: TypePub Label: Publication Type Group: TypPub Data: Journal Article; Review – Name: Language Label: Language Group: Lang Data: English – Name: TitleSource Label: Journal Info Group: Src Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Humana+Press%22">Humana Press </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>9214969 <i>Publication Model: </i>Print <i>Cited Medium: </i>Internet <i>ISSN: </i>1940-6029 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2210643745%22">10643745 </searchLink><i>NLM ISO Abbreviation: </i>Methods Mol Biol <i>Subsets: </i>MEDLINE – Name: PublisherInfo Label: Imprint Name(s) Group: PubInfo Data: <i>Publication</i>: Totowa, NJ : Humana Press<br /><i>Original Publication</i>: Clifton, N.J. : Humana Press – Name: SubjectMESH Label: MeSH Terms Group: Su Data: <searchLink fieldCode="MM" term="%22Comparative+Genomic+Hybridization%22">Comparative Genomic Hybridization*</searchLink>/<searchLink fieldCode="MM" term="%22Comparative+Genomic+Hybridization+methods%22">methods</searchLink> <br /><searchLink fieldCode="MM" term="%22Toxicogenetics%22">Toxicogenetics*</searchLink>/<searchLink fieldCode="MM" term="%22Toxicogenetics+methods%22">methods</searchLink><br /><searchLink fieldCode="MH" term="%22High-Throughput+Nucleotide+Sequencing%22">High-Throughput Nucleotide Sequencing</searchLink>/<searchLink fieldCode="MH" term="%22High-Throughput+Nucleotide+Sequencing+methods%22">methods</searchLink> ; <searchLink fieldCode="MH" term="%22Mutagenicity+Tests%22">Mutagenicity Tests</searchLink>/<searchLink fieldCode="MH" term="%22Mutagenicity+Tests+methods%22">methods</searchLink> ; <searchLink fieldCode="MH" term="%22Genomics%22">Genomics</searchLink>/<searchLink fieldCode="MH" term="%22Genomics+methods%22">methods</searchLink> ; <searchLink fieldCode="MH" term="%22Gene+Editing%22">Gene Editing</searchLink>/<searchLink fieldCode="MH" term="%22Gene+Editing+methods%22">methods</searchLink> ; <searchLink fieldCode="MH" term="%22Humans%22">Humans</searchLink> ; <searchLink fieldCode="MH" term="%22DNA+Copy+Number+Variations%22">DNA Copy Number Variations</searchLink> ; <searchLink fieldCode="MH" term="%22Machine+Learning%22">Machine Learning</searchLink> ; <searchLink fieldCode="MH" term="%22Animals%22">Animals</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Over the past two decades, comparative genomic hybridization (CGH) and array CGH have become essential tools in clinical diagnostics, oncology, and toxicological risk assessment. Initially developed to identify chromosomal imbalances like copy number variations (CNVs) in tumor cells, these technologies have expanded into genotoxicology and toxicogenomics, exploring gene responses to toxic agents and their molecular mechanisms. As of 2024, new developments include integrating array CGH with next-generation sequencing (NGS), machine learning, and CRISPR-Cas9 genome editing, greatly improving precision. High-density CGH arrays now offer single-cell resolution, enabling the detection of cellular heterogeneity in toxic responses, while long-read sequencing facilitates the identification of complex genomic rearrangements. Recent innovations include combining CGH and toxicogenomics with organ-on-chip models for real-time, tissue-specific toxicological assessment. This has significantly improved the relevance of toxicological data for human health. However, while these advances are promising, array CGH remains costly and requires substantial data processing, driving the need for advanced bioinformatics tools. AI-driven predictive toxicology models are also gaining traction, correlating toxicogenomic profiles with clinical outcomes. Despite these advancements, the field still faces challenges, such as evolving regulatory guidelines and complex data interpretation, which hinder broader adoption and the full realization of CGH's potential in toxicology and risk assessment.<br /> (© 2026. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.) – Name: Ref Label: References Group: RefInfo Data: Pinkel D, Straume T, Gray JW (1986) Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci USA 83(9):2934–2938. (PMID: <searchLink fieldCode="PM" term="%22345825432342110%2E1073%2Fpnas%2E83%2E9%2E2934%22">345825432342110.1073/pnas.83.9.2934)</searchLink><br />Laan M, Kallioniemi OP, Hellsten E et al (1995) Mechanically stretched chromosomes as targets for high-resolution FISH mapping. Genome Res 5(1):13–20. (PMID: <searchLink fieldCode="PM" term="%22871705110%2E1101%2Fgr%2E5%2E1%2E13%22">871705110.1101/gr.5.1.13)</searchLink><br />Pang AW, MacDonald JR, Pinto D et al (2010) Towards a comprehensive structural variation map of an individual human genome. Genome Biol 11(5):R52. (PMID: <searchLink fieldCode="PM" term="%2220482838289806510%2E1186%2Fgb-2010-11-5-r52%22">20482838289806510.1186/gb-2010-11-5-r52)</searchLink><br />Raap AK, Tanke HJ (2006) COmbined Binary RAtio fluorescence in situ hybridiziation (COBRA-FISH): development and applications. Cytogenet Genome Res 114(3–4):222–226. (PMID: <searchLink fieldCode="PM" term="%221695465710%2E1159%2F000094204%22">1695465710.1159/000094204)</searchLink><br />Heng HH, Squire J, Tsui LC (1992) High-resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc Natl Acad Sci USA 89(20):9509–9513. (PMID: <searchLink fieldCode="PM" term="%2213840555016110%2E1073%2Fpnas%2E89%2E20%2E9509%22">13840555016110.1073/pnas.89.20.9509)</searchLink><br />Schrock E, du Manoir S, Veldman T et al (1996) Multicolor spectral karyotyping of human chromosomes. Science 273(5274):494–497. (PMID: <searchLink fieldCode="PM" term="%22866253710%2E1126%2Fscience%2E273%2E5274%2E494%22">866253710.1126/science.273.5274.494)</searchLink><br />Speicher MR, Gwyn Ballard S, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12(4):368–375. (PMID: <searchLink fieldCode="PM" term="%22863048910%2E1038%2Fng0496-368%22">863048910.1038/ng0496-368)</searchLink><br />Bolzer A, Kreth G, Solovei I et al (2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3(5):e157. (PMID: <searchLink fieldCode="PM" term="%2215839726108433510%2E1371%2Fjournal%2Epbio%2E0030157%22">15839726108433510.1371/journal.pbio.0030157)</searchLink><br />Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2(4):292–301. (PMID: <searchLink fieldCode="PM" term="%221128370110%2E1038%2F35066075%22">1128370110.1038/35066075)</searchLink><br />Chen B, Gilbert LA, Cimini BA et al (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155(7):1479–1491. (PMID: <searchLink fieldCode="PM" term="%2224360272391850210%2E1016%2Fj%2Ecell%2E2013%2E12%2E001%22">24360272391850210.1016/j.cell.2013.12.001)</searchLink><br />Deng W, Shi X, Tjian R et al (2015) CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. Proc Natl Acad Sci USA 112(38):11870–11875. (PMID: <searchLink fieldCode="PM" term="%2226324940458683710%2E1073%2Fpnas%2E1515692112%22">26324940458683710.1073/pnas.1515692112)</searchLink><br />Huang Y, Fernandez SV, Goodwin S et al (2007) Epithelial to mesenchymal transition in human breast epithelial cells transformed by 17beta-estradiol. Cancer Res 67(23):11147–11157. (PMID: <searchLink fieldCode="PM" term="%221805643910%2E1158%2F0008-5472%2ECAN-07-1371%22">1805643910.1158/0008-5472.CAN-07-1371)</searchLink><br />Kallioniemi A, Kallioniemi OP, Sudar D et al (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258(5083):818–821. (PMID: <searchLink fieldCode="PM" term="%22135964110%2E1126%2Fscience%2E1359641%22">135964110.1126/science.1359641)</searchLink><br />Pinkel D, Segraves R, Sudar D et al (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20(2):207–211. (PMID: <searchLink fieldCode="PM" term="%22977171810%2E1038%2F2524%22">977171810.1038/2524)</searchLink><br />Albertini RJ, Anderson D, Douglas GR et al (2000) IPCS guidelines for the monitoring of genotoxic effects of carcinogens in humans. International Programme on Chemical Safety. Mutat Res 463(2):111–172. (PMID: <searchLink fieldCode="PM" term="%221091390810%2E1016%2FS1383-5742%2800%2900049-1%22">1091390810.1016/S1383-5742(00)00049-1)</searchLink><br />Zhao EY, Jones M, Jones SJM (2019) Whole-genome sequencing in cancer. Cold Spring Harb Perspect Med 9(3):a034579. (PMID: <searchLink fieldCode="PM" term="%2229844223639634310%2E1101%2Fcshperspect%2Ea034579%22">29844223639634310.1101/cshperspect.a034579)</searchLink><br />van Delft J, Gaj S, Lienhard M et al (2012) RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene. Toxicol Sci 130(2):427–439. (PMID: <searchLink fieldCode="PM" term="%222288981110%2E1093%2Ftoxsci%2Fkfs250%22">2288981110.1093/toxsci/kfs250)</searchLink><br />Kreuzer K, Sprenger H, Braeuning A (2022) Comparative analysis of transcriptional responses to genotoxic and non-genotoxic agents in the blood cell model TK6 and the liver model HepaRG. Int J Mol Sci 23(7):3420. (PMID: <searchLink fieldCode="PM" term="%2235408779899874510%2E3390%2Fijms23073420%22">35408779899874510.3390/ijms23073420)</searchLink><br />Afshari CA, Hamadeh HK, Bushel PR (2011) The evolution of bioinformatics in toxicology: advancing toxicogenomics. Toxicol Sci 120(Suppl 1):S225–S237. (PMID: <searchLink fieldCode="PM" term="%222117777510%2E1093%2Ftoxsci%2Fkfq373%22">2117777510.1093/toxsci/kfq373)</searchLink><br />Skardal A (2024) Grand challenges in organoid and organ-on-a-chip technologies. Front Bioeng Biotechnol 12:1366280. (PMID: <searchLink fieldCode="PM" term="%22384560041091939910%2E3389%2Ffbioe%2E2024%2E1366280%22">384560041091939910.3389/fbioe.2024.1366280)</searchLink><br />Zhao Y, Lann S, Okhovatian S et al (2024) Integrating organoids and organ-on-a-chip devices. Nat Rev Bioeng 2:588–608. (PMID: <searchLink fieldCode="PM" term="%2210%2E1038%2Fs44222-024-00207-z%22">10.1038/s44222-024-00207-z)</searchLink><br />Maqsood K, Hagras H, Radu Zabet N (2024) An overview of artifcial intelligence in the feld of genomics. Discov Artif Intell 4:9. (PMID: <searchLink fieldCode="PM" term="%2210%2E1007%2Fs44163-024-00103-w%22">10.1007/s44163-024-00103-w)</searchLink><br />Pinkel D, Albertson DG (2005) Comparative genomic hybridization. Annu Rev Genomics Hum Genet 6:331–354. (PMID: <searchLink fieldCode="PM" term="%221612486510%2E1146%2Fannurev%2Egenom%2E6%2E080604%2E162140%22">1612486510.1146/annurev.genom.6.080604.162140)</searchLink><br />Schmeisser S, Miccoli A, von Bergen M et al (2023) New approach methodologies in human regulatory toxicology – not if, but how and when! Environ Int 178:108082. (PMID: <searchLink fieldCode="PM" term="%22374229751085868310%2E1016%2Fj%2Eenvint%2E2023%2E108082%22">374229751085868310.1016/j.envint.2023.108082)</searchLink><br />du Manoir S, Speicher MR, Joos S et al (1993) Detection of complete and partial chromosome gains and losses by comparative genomic in situ hybridization. Hum Genet 90(6):590–610. (PMID: <searchLink fieldCode="PM" term="%22844446510%2E1007%2FBF00202476%22">844446510.1007/BF00202476)</searchLink><br />Redon R, Carter NP (2009) Comparative genomic hybridization: microarray design and data interpretation. Methods Mol Biol 529:37–49. (PMID: <searchLink fieldCode="PM" term="%2219381971287131010%2E1007%2F978-1-59745-538-1%26#95%3B3%22">19381971287131010.1007/978-1-59745-538-1&#95;3)</searchLink><br />Aradhya S, Cherry AM (2007) Array-based comparative genomic hybridization: clinical contexts for targeted and whole-genome designs. Genet Med 9(9):553–559. (PMID: <searchLink fieldCode="PM" term="%221787364210%2E1097%2FGIM%2E0b013e318149e354%22">1787364210.1097/GIM.0b013e318149e354)</searchLink><br />Carreira IM, Ferreira SI, Matoso E et al (2015) Copy number variants prioritization after array-CGH analysis – a cohort of 1000 patients. Mol Cytogenet 8:103. (PMID: <searchLink fieldCode="PM" term="%2226719768469624710%2E1186%2Fs13039-015-0202-z%22">26719768469624710.1186/s13039-015-0202-z)</searchLink><br />Wa CV, DeVries S, Chen YY et al (2005) Clinical application of array-based comparative genomic hybridization to define the relationship between multiple synchronous tumors. Mod Pathol 18(4):591–597. (PMID: <searchLink fieldCode="PM" term="%221569612910%2E1038%2Fmodpathol%2E3800332%22">1569612910.1038/modpathol.3800332)</searchLink><br />Pinkel D, Albertson DG (2005) Array comparative genomic hybridization and its applications in cancer. Nat Genet 37(Suppl):S11–S17. (PMID: <searchLink fieldCode="PM" term="%221592052410%2E1038%2Fng1569%22">1592052410.1038/ng1569)</searchLink><br />Albertson DG, Ylstra B, Segraves R et al (2000) Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet 25(2):144–146. (PMID: <searchLink fieldCode="PM" term="%221083562610%2E1038%2F75985%22">1083562610.1038/75985)</searchLink><br />Han W, Jung EM, Cho J et al (2008) DNA copy number alterations and expression of relevant genes in triple-negative breast cancer. Genes Chromosomes Cancer 47(6):490–499. (PMID: <searchLink fieldCode="PM" term="%221831490810%2E1002%2Fgcc%2E20550%22">1831490810.1002/gcc.20550)</searchLink><br />Snijders AM, Nowak N, Segraves R et al (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29(3):263–264. (PMID: <searchLink fieldCode="PM" term="%221168779510%2E1038%2Fng754%22">1168779510.1038/ng754)</searchLink><br />Baslan T, Kendall J, Rodgers L et al (2012) Genome-wide copy number analysis of single cells. Nat Protoc 7(6):1024–1041. (PMID: <searchLink fieldCode="PM" term="%2222555242506970110%2E1038%2Fnprot%2E2012%2E039%22">22555242506970110.1038/nprot.2012.039)</searchLink><br />Masset H, Ding J, Dimitriadou E et al (2022) Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing. Nucleic Acids Res 50(11):e63. (PMID: <searchLink fieldCode="PM" term="%2235212381922649510%2E1093%2Fnar%2Fgkac134%22">35212381922649510.1093/nar/gkac134)</searchLink><br />Carter NP (2007) Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 39(7 Suppl):S16–S21. (PMID: <searchLink fieldCode="PM" term="%2217597776269749410%2E1038%2Fng2028%22">17597776269749410.1038/ng2028)</searchLink><br />Schoumans J, Nielsen K, Jeppesen I et al (2004) A comparison of different metaphase CGH methods for the detection of cryptic chromosome aberrations of defined size. Eur J Hum Genet 12(6):447–454. (PMID: <searchLink fieldCode="PM" term="%221502678410%2E1038%2Fsj%2Eejhg%2E5201175%22">1502678410.1038/sj.ejhg.5201175)</searchLink><br />Tachdjian G, Aboura A, Lapierre JM et al (2000) Cytogenetic analysis from DNA by comparative genomic hybridization. Ann Genet 43(3–4):147–154. (PMID: <searchLink fieldCode="PM" term="%221116419710%2E1016%2FS0003-3995%2800%2901028-5%22">1116419710.1016/S0003-3995(00)01028-5)</searchLink><br />Kallioniemi OP, Kallioniemi A, Sudar D et al (1993) Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin Cancer Biol 4(1):41–46. (PMID: <searchLink fieldCode="PM" term="%228448377%22">8448377)</searchLink><br />Piper J, Rutovitz D, Sudar D et al (1995) Computer image analysis of comparative genomic hybridization. Cytometry 19(1):10–26. (PMID: <searchLink fieldCode="PM" term="%22770518110%2E1002%2Fcyto%2E990190104%22">770518110.1002/cyto.990190104)</searchLink><br />Zitzelsberger H, Lehmann L, Werner M et al (1997) Comparative genomic hybridisation for the analysis of chromosomal imbalances in solid tumours and haematological malignancies. Histochem Cell Biol 108(4–5):403–417. (PMID: <searchLink fieldCode="PM" term="%22938793310%2E1007%2Fs004180050181%22">938793310.1007/s004180050181)</searchLink><br />Martinez-Granero F, Blanco-Kelly F, Sanchez-Jimeno C et al (2021) Comparison of the diagnostic yield of aCGH and genome-wide sequencing across different neurodevelopmental disorders. NPJ Genom Med 6(1):25. (PMID: <searchLink fieldCode="PM" term="%2233767182799471310%2E1038%2Fs41525-021-00188-7%22">33767182799471310.1038/s41525-021-00188-7)</searchLink><br />Michels E, De Preter K, Van Roy N et al (2007) Detection of DNA copy number alterations in cancer by array comparative genomic hybridization. Genet Med 9(9):574–584. (PMID: <searchLink fieldCode="PM" term="%221787364510%2E1097%2FGIM%2E0b013e318145b25b%22">1787364510.1097/GIM.0b013e318145b25b)</searchLink><br />Shakoori AR (2017) Fluorescence in situ hybridization (FISH) and its applications. In: Bhat TA, Wani AA (eds) Chromosome structure and aberrations. Springer, pp 343–367. (PMID: <searchLink fieldCode="PM" term="%2210%2E1007%2F978-81-322-3673-3%26#95%3B16%22">10.1007/978-81-322-3673-3&#95;16)</searchLink><br />Jobanputra V, Kriplani A, Choudhry VP et al (1998) Detection of chromosomal abnormalities using fluorescence in situ hybridization (FISH). Natl Med J India 11(6):259–263. (PMID: <searchLink fieldCode="PM" term="%2210083791%22">10083791)</searchLink><br />Lee VC, Chow JF, Lau EY et al (2015) Comparison between fluorescent in-situ hybridisation and array comparative genomic hybridisation in preimplantation genetic diagnosis in translocation carriers. Hong Kong Med J 21(1):16–22. (PMID: <searchLink fieldCode="PM" term="%2225345996%22">25345996)</searchLink><br />Sugimura H (2008) Detection of chromosome changes in pathology archives: an application of microwave-assisted fluorescence in situ hybridization to human carcinogenesis studies. Carcinogenesis 29(4):681–687. (PMID: <searchLink fieldCode="PM" term="%221828304210%2E1093%2Fcarcin%2Fbgn046%22">1828304210.1093/carcin/bgn046)</searchLink><br />Larramendy ML, El-Rifai W, Knuutila S (1998) Comparison of fluorescein isothiocyanate- and Texas red-conjugated nucleotides for direct labeling in comparative genomic hybridization. Cytometry 31(3):174–179. (PMID: <searchLink fieldCode="PM" term="%22951571610%2E1002%2F%28SICI%291097-0320%2819980301%2931%3A3%26lt%3B174%3A%3AAID-CYTO4%26gt%3B3%2E0%2ECO%3B2-L%22">951571610.1002/(SICI)1097-0320(19980301)31:3&lt;174::AID-CYTO4&gt;3.0.CO;2-L)</searchLink><br />Berisha SZ, Shetty S, Prior TW et al (2020) Cytogenetic and molecular diagnostic testing associated with prenatal and postnatal birth defects. Birth Defects Res 112(4):293–306. (PMID: <searchLink fieldCode="PM" term="%2232115903929095410%2E1002%2Fbdr2%2E1648%22">32115903929095410.1002/bdr2.1648)</searchLink><br />Miller DT, Adam MP, Aradhya S et al (2010) Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 86(5):749–764. (PMID: <searchLink fieldCode="PM" term="%2220466091286900010%2E1016%2Fj%2Eajhg%2E2010%2E04%2E006%22">20466091286900010.1016/j.ajhg.2010.04.006)</searchLink><br />Zhao M, Wang Q, Wang Q et al (2013) Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics 14(Suppl 11):S1. (PMID: <searchLink fieldCode="PM" term="%2224564169384687810%2E1186%2F1471-2105-14-S11-S1%22">24564169384687810.1186/1471-2105-14-S11-S1)</searchLink><br />Chiang DY, Getz G, Jaffe DB et al (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6(1):99–103. (PMID: <searchLink fieldCode="PM" term="%221904341210%2E1038%2Fnmeth%2E1276%22">1904341210.1038/nmeth.1276)</searchLink><br />Stefanicka-Wojtas D, Kurpas D (2023) Personalised medicine-implementation to the healthcare system in Europe (focus group discussions). J Pers Med 13(3):380. (PMID: <searchLink fieldCode="PM" term="%22369835621005856810%2E3390%2Fjpm13030380%22">369835621005856810.3390/jpm13030380)</searchLink><br />Shao L, Kang SH, Li J et al (2010) Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics. J Mol Diagn 12(5):670–679. (PMID: <searchLink fieldCode="PM" term="%2220724749292843210%2E2353%2Fjmoldx%2E2010%2E090192%22">20724749292843210.2353/jmoldx.2010.090192)</searchLink><br />Lingjaerde OC, Baumbusch LO, Liestol K et al (2005) CGH-explorer: a program for analysis of array-CGH data. Bioinformatics 21(6):821–822. (PMID: <searchLink fieldCode="PM" term="%221553161010%2E1093%2Fbioinformatics%2Fbti113%22">1553161010.1093/bioinformatics/bti113)</searchLink><br />Solinas-Toldo S, Lampel S, Stilgenbauer S et al (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20(4):399–407. (PMID: <searchLink fieldCode="PM" term="%22940875710%2E1002%2F%28SICI%291098-2264%28199712%2920%3A4%26lt%3B399%3A%3AAID-GCC12%26gt%3B3%2E0%2ECO%3B2-I%22">940875710.1002/(SICI)1098-2264(199712)20:4&lt;399::AID-GCC12&gt;3.0.CO;2-I)</searchLink><br />Chen W, Erdogan F, Ropers HH et al (2005) CGHPRO – a comprehensive data analysis tool for array CGH. BMC Bioinformatics 6:85. (PMID: <searchLink fieldCode="PM" term="%2215807904127426810%2E1186%2F1471-2105-6-85%22">15807904127426810.1186/1471-2105-6-85)</searchLink><br />Fridlyand J, Snijders AM, Pinkel D et al (2004) Hidden Markov models approach to the analysis of array CGH data. J Multivar Anal 90(1):132–153. (PMID: <searchLink fieldCode="PM" term="%2210%2E1016%2Fj%2Ejmva%2E2004%2E02%2E008%22">10.1016/j.jmva.2004.02.008)</searchLink><br />Liva S, Hupe P, Neuvial P et al (2006) CAPweb: a bioinformatics CGH array analysis platform. Nucleic Acids Res 34(Web Server issue):W477–W481. (PMID: <searchLink fieldCode="PM" term="%2216845053153885210%2E1093%2Fnar%2Fgkl215%22">16845053153885210.1093/nar/gkl215)</searchLink><br />Riggs ER, Andersen EF, Cherry AM et al (2020) Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med 22(2):245–257. (PMID: <searchLink fieldCode="PM" term="%223169083510%2E1038%2Fs41436-019-0686-8%22">3169083510.1038/s41436-019-0686-8)</searchLink><br />Komura D, Shen F, Ishikawa S et al (2006) Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res 16(12):1575–1584. (PMID: <searchLink fieldCode="PM" term="%2217122084166564110%2E1101%2Fgr%2E5629106%22">17122084166564110.1101/gr.5629106)</searchLink><br />Jones JA, McMahon NP, Zheng T et al (2021) Oligonucleotide conjugated antibody strategies for cyclic immunostaining. Sci Rep 11(1):23844. (PMID: <searchLink fieldCode="PM" term="%2234903759866895610%2E1038%2Fs41598-021-03135-9%22">34903759866895610.1038/s41598-021-03135-9)</searchLink><br />Theisen A (2008) Microarray-based comparative genomic hybridization (aCGH). Nat Educ 1(1):45.<br />Harper JC, Harton G (2010) The use of arrays in preimplantation genetic diagnosis and screening. Fertil Steril 94(4):1173–1177. (PMID: <searchLink fieldCode="PM" term="%222057964110%2E1016%2Fj%2Efertnstert%2E2010%2E04%2E064%22">2057964110.1016/j.fertnstert.2010.04.064)</searchLink><br />Van der Aa N, Zamani Esteki M, Vermeesch JR et al (2013) Preimplantation genetic diagnosis guided by single-cell genomics. Genome Med 5(8):71. (PMID: <searchLink fieldCode="PM" term="%2223998893397912210%2E1186%2Fgm475%22">23998893397912210.1186/gm475)</searchLink><br />Tsuiko O, Fernandez Gallardo E, Voet T et al (2020) Preimplantation genetic testing: single-cell technologies at the forefront of PGT and embryo research. Reproduction 160(5):A19–A31. (PMID: <searchLink fieldCode="PM" term="%223306554510%2E1530%2FREP-20-0102%22">3306554510.1530/REP-20-0102)</searchLink><br />Bejjani BA, Shaffer LG (2006) Application of array-based comparative genomic hybridization to clinical diagnostics. J Mol Diagn 8(5):528–533. (PMID: <searchLink fieldCode="PM" term="%2217065418187617610%2E2353%2Fjmoldx%2E2006%2E060029%22">17065418187617610.2353/jmoldx.2006.060029)</searchLink><br />Levy B, Wapner R (2018) Prenatal diagnosis by chromosomal microarray analysis. Fertil Steril 109(2):201–212. (PMID: <searchLink fieldCode="PM" term="%2229447663585615410%2E1016%2Fj%2Efertnstert%2E2018%2E01%2E005%22">29447663585615410.1016/j.fertnstert.2018.01.005)</searchLink><br />Herzog CR, Desai D, Amin S (2006) Array CGH analysis reveals chromosomal aberrations in mouse lung adenocarcinomas induced by the human lung carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Biochem Biophys Res Commun 341(3):856–863. (PMID: <searchLink fieldCode="PM" term="%221645505610%2E1016%2Fj%2Ebbrc%2E2006%2E01%2E043%22">1645505610.1016/j.bbrc.2006.01.043)</searchLink><br />Heinloth AN, Shackelford RE, Innes CL et al (2003) ATM-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and UV irradiation. Radiat Res 160(3):273–290. (PMID: <searchLink fieldCode="PM" term="%221292698610%2E1667%2FRR3047%22">1292698610.1667/RR3047)</searchLink><br />Brown N, Finnon R, Manning G et al (2015) Influence of radiation quality on mouse chromosome 2 deletions in radiation-induced acute myeloid leukaemia. Mutat Res Genet Toxicol Environ Mutagen 793:48–54. (PMID: <searchLink fieldCode="PM" term="%222652037210%2E1016%2Fj%2Emrgentox%2E2015%2E07%2E012%22">2652037210.1016/j.mrgentox.2015.07.012)</searchLink><br />Cooper CS (2001) Applications of microarray technology in breast cancer research. Breast Cancer Res 3(3):158–175. (PMID: <searchLink fieldCode="PM" term="%221130595113868110%2E1186%2Fbcr291%22">1130595113868110.1186/bcr291)</searchLink><br />Coughlin CR 2nd, Scharer GH, Shaikh TH (2012) Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns. Genome Med 4(10):80. (PMID: <searchLink fieldCode="PM" term="%2223114084358044910%2E1186%2Fgm381%22">23114084358044910.1186/gm381)</searchLink><br />Wang H, Chen L, Li D et al (2017) Microarray analysis of lung long non-coding RNAs in cigarette smoke-exposed mouse model. Oncotarget 8(70):115647–115656. (PMID: <searchLink fieldCode="PM" term="%2229383188577780010%2E18632%2Foncotarget%2E23362%22">29383188577780010.18632/oncotarget.23362)</searchLink><br />Szabo RT, Kovacs-Weber M, Balogh KM et al (2024) Effect of aflatoxin B1 and sterigmatocystin on DNA repair genes in common carp. Aquat Toxicol 276:107076. (PMID: <searchLink fieldCode="PM" term="%223927799210%2E1016%2Fj%2Eaquatox%2E2024%2E107076%22">3927799210.1016/j.aquatox.2024.107076)</searchLink><br />Brennan KM, Oh SY, Yiannikouris A et al (2017) Differential gene expression analysis of bovine macrophages after exposure to the Penicillium mycotoxins citrinin and/or ochratoxin A. Toxins (Basel) 9(11):366. (PMID: <searchLink fieldCode="PM" term="%2229137202570598110%2E3390%2Ftoxins9110366%22">29137202570598110.3390/toxins9110366)</searchLink><br />Hester SD, Reid L, Nowak N et al (2009) Comparison of comparative genomic hybridization technologies across microarray platforms. J Biomol Tech 20(2):135–151. (PMID: <searchLink fieldCode="PM" term="%22195036252685605%22">195036252685605)</searchLink><br />Baken KA, Vandebriel RJ, Pennings JL et al (2007) Toxicogenomics in the assessment of immunotoxicity. Methods 41(1):132–141. (PMID: <searchLink fieldCode="PM" term="%221716131010%2E1016%2Fj%2Eymeth%2E2006%2E07%2E010%22">1716131010.1016/j.ymeth.2006.07.010)</searchLink><br />Milan M, Coppe A, Reinhardt R et al (2011) Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring. BMC Genomics 12:234. (PMID: <searchLink fieldCode="PM" term="%2221569398310781510%2E1186%2F1471-2164-12-234%22">21569398310781510.1186/1471-2164-12-234)</searchLink><br />Shah SP, Xuan X, DeLeeuw RJ et al (2006) Integrating copy number polymorphisms into array CGH analysis using a robust HMM. Bioinformatics 22(14):e431–e439. (PMID: <searchLink fieldCode="PM" term="%221687350410%2E1093%2Fbioinformatics%2Fbtl238%22">1687350410.1093/bioinformatics/btl238)</searchLink><br />Guha S, Li Y, Neuberg D (2008) Bayesian hidden Markov modeling of array CGH data. J Am Stat Assoc 103(482):485–497. (PMID: <searchLink fieldCode="PM" term="%2222375091328662210%2E1198%2F016214507000000923%22">22375091328662210.1198/016214507000000923)</searchLink><br />Vermeesch JR, Melotte C, Froyen G et al (2005) Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis. J Histochem Cytochem 53(3):413–422. (PMID: <searchLink fieldCode="PM" term="%221575003110%2E1369%2Fjhc%2E4A6436%2E2005%22">1575003110.1369/jhc.4A6436.2005)</searchLink><br />Shaw-Smith C, Redon R, Rickman L et al (2004) Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 41(4):241–248. (PMID: <searchLink fieldCode="PM" term="%2215060094173572610%2E1136%2Fjmg%2E2003%2E017731%22">15060094173572610.1136/jmg.2003.017731)</searchLink><br />Brazma A (2009) Minimum information about a microarray experiment (MIAME)-successes, failures, challenges. ScientificWorldJournal 9:420–423. (PMID: <searchLink fieldCode="PM" term="%2219484163582322410%2E1100%2Ftsw%2E2009%2E57%22">19484163582322410.1100/tsw.2009.57)</searchLink><br />Brazma A, Hingamp P, Quackenbush J et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29(4):365–371. (PMID: <searchLink fieldCode="PM" term="%221172692010%2E1038%2Fng1201-365%22">1172692010.1038/ng1201-365)</searchLink><br />Liu Y, Li A, Feng H et al (2015) TAFFYS: an integrated tool for comprehensive analysis of genomic aberrations in tumor samples. PLoS One 10(6):e0129835. (PMID: <searchLink fieldCode="PM" term="%2226111017448239410%2E1371%2Fjournal%2Epone%2E0129835%22">26111017448239410.1371/journal.pone.0129835)</searchLink><br />Quigley D (2015) Equalizer reduces SNP bias in Affymetrix microarrays. BMC Bioinformatics 16:238. (PMID: <searchLink fieldCode="PM" term="%2226223252451888910%2E1186%2Fs12859-015-0669-y%22">26223252451888910.1186/s12859-015-0669-y)</searchLink><br />Mayrhofer M, Viklund B, Isaksson A (2016) Rawcopy: improved copy number analysis with Affymetrix arrays. Sci Rep 6:36158. (PMID: <searchLink fieldCode="PM" term="%2227796336508694010%2E1038%2Fsrep36158%22">27796336508694010.1038/srep36158)</searchLink><br />Morgan AP (2015) argyle: an R package for analysis of illumina genotyping arrays. G3 (Bethesda) 6(2):281–286. (PMID: <searchLink fieldCode="PM" term="%2226684930475154810%2E1534%2Fg3%2E115%2E023739%22">26684930475154810.1534/g3.115.023739)</searchLink><br />Chan VSW, Theilade MD (2005) The use of toxicogenomic data in risk assessment: a regulatory perspective. Clin Toxicol 43(2):121–126. (PMID: <searchLink fieldCode="PM" term="%2210%2E1081%2FCLT-50407%22">10.1081/CLT-50407)</searchLink><br />Tice RR, Austin CP, Kavlock RJ et al (2013) Improving the human hazard characterization of chemicals: a Tox21 update. Environ Health Perspect 121(7):756–765. (PMID: <searchLink fieldCode="PM" term="%2223603828370199210%2E1289%2Fehp%2E1205784%22">23603828370199210.1289/ehp.1205784)</searchLink><br />Aardema MJ, MacGregor JT (2002) Toxicology and genetic toxicology in the new era of “toxicogenomics”: impact of “-omics” technologies. Mutat Res 499(1):13–25. (PMID: <searchLink fieldCode="PM" term="%2211804602%22">11804602)</searchLink><br />Davis AP, King BL, Mockus S et al (2011) The comparative toxicogenomics database: update 2011. Nucleic Acids Res 39(Database issue):D1067–D1072. (PMID: <searchLink fieldCode="PM" term="%222086444810%2E1093%2Fnar%2Fgkq813%22">2086444810.1093/nar/gkq813)</searchLink><br />Nuwaysir EF, Bittner M, Trent J et al (1999) Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog 24(3):153–159. (PMID: <searchLink fieldCode="PM" term="%221020479910%2E1002%2F%28SICI%291098-2744%28199903%2924%3A3%26lt%3B153%3A%3AAID-MC1%26gt%3B3%2E0%2ECO%3B2-P%22">1020479910.1002/(SICI)1098-2744(199903)24:3&lt;153::AID-MC1&gt;3.0.CO;2-P)</searchLink><br />Lettieri T (2006) Recent applications of DNA microarray technology to toxicology and ecotoxicology. Environ Health Perspect 114(1):4–9. (PMID: <searchLink fieldCode="PM" term="%2216393650133264810%2E1289%2Fehp%2E8194%22">16393650133264810.1289/ehp.8194)</searchLink><br />Gerhold D, Lu MQ, Xu J et al (2001) Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays. Physiol Genomics 5(4):161–170. (PMID: <searchLink fieldCode="PM" term="%221132896110%2E1152%2Fphysiolgenomics%2E2001%2E5%2E4%2E161%22">1132896110.1152/physiolgenomics.2001.5.4.161)</searchLink><br />OECD (2009) Series on testing and assessment no. 100 – report of the second survey on available omics tools (ENV/JM/MONO(2008)35). Available at http://www.oecd.org/officialdocuments/displaydocument/?cote=env/jm/mono(2008)35&doclanguage=en . Accessed: 22 June 2018.<br />Vrana KE, Freeman WM, Aschner M (2003) Use of microarray technologies in toxicology research. Neurotoxicology 24(3):321–332. (PMID: <searchLink fieldCode="PM" term="%221278209810%2E1016%2FS0161-813X%2802%2900193-6%22">1278209810.1016/S0161-813X(02)00193-6)</searchLink><br />Awuah WA, Shah MH, Sanker V et al (2025) Advances in chromosomal microarray analysis: transforming neurology and neurosurgery. Brain Spine 5:104197. (PMID: <searchLink fieldCode="PM" term="%22399901161184712610%2E1016%2Fj%2Ebas%2E2025%2E104197%22">399901161184712610.1016/j.bas.2025.104197)</searchLink><br />EMBL (2025) Highlights 2024. Available at https://www.embl.org/documents/wp-content/uploads/2025/03/EMBL-EBI-Highlights-Report-2024.pdf . Accessed: 9 June 2025.<br />Bottosso M, Mosele F, Michiels S et al (2024) Moving toward precision medicine to predict drug sensitivity in patients with metastatic breast cancer. ESMO Open 9(3):102247. (PMID: <searchLink fieldCode="PM" term="%22384012481098286310%2E1016%2Fj%2Eesmoop%2E2024%2E102247%22">384012481098286310.1016/j.esmoop.2024.102247)</searchLink><br />Pereira R, Oliveira J, Sousa M (2020) Bioinformatics and computational tools for next-generation sequencing analysis in clinical genetics. J Clin Med 9(1):132. (PMID: <searchLink fieldCode="PM" term="%2231947757701934910%2E3390%2Fjcm9010132%22">31947757701934910.3390/jcm9010132)</searchLink><br />Davis AP, Grondin CJ, Johnson RJ et al (2017) The comparative toxicogenomics database: update 2017. Nucleic Acids Res 45(D1):D972–D978. (PMID: <searchLink fieldCode="PM" term="%222765145710%2E1093%2Fnar%2Fgkw838%22">2765145710.1093/nar/gkw838)</searchLink><br />Mattingly CJ, Rosenstein MC, Davis AP et al (2006) The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. Toxicol Sci 92(2):587–595. (PMID: <searchLink fieldCode="PM" term="%2216675512158611110%2E1093%2Ftoxsci%2Fkfl008%22">16675512158611110.1093/toxsci/kfl008)</searchLink><br />Davis AP, Wiegers TC, Wiegers J et al (2018) Chemical-induced phenotypes at CTD help inform the predisease state and construct adverse outcome pathways. Toxicol Sci 165(1):145–156. (PMID: <searchLink fieldCode="PM" term="%2229846728611178710%2E1093%2Ftoxsci%2Fkfy131%22">29846728611178710.1093/toxsci/kfy131)</searchLink><br />Grondin CJ, Davis AP, Wiegers TC et al (2018) Accessing an expanded exposure science module at the comparative toxicogenomics database. Environ Health Perspect 126(1):014501. (PMID: <searchLink fieldCode="PM" term="%2229351546601468810%2E1289%2FEHP2873%22">29351546601468810.1289/EHP2873)</searchLink><br />Young RR (2002) Genetic toxicology: web resources. Toxicology 173(1–2):103–121. (PMID: <searchLink fieldCode="PM" term="%221195568810%2E1016%2FS0300-483X%2802%2900026-4%22">1195568810.1016/S0300-483X(02)00026-4)</searchLink><br />Lea IA, Gong H, Paleja A et al (2017) CEBS: a comprehensive annotated database of toxicological data. Nucleic Acids Res 45(D1):D964–D971. (PMID: <searchLink fieldCode="PM" term="%222789966010%2E1093%2Fnar%2Fgkw1077%22">2789966010.1093/nar/gkw1077)</searchLink><br />Andersen ME, Al-Zoughool M, Croteau M et al (2010) The future of toxicity testing. J Toxicol Environ Health B Crit Rev 13(2–4):163–196. (PMID: <searchLink fieldCode="PM" term="%222057489610%2E1080%2F10937404%2E2010%2E483933%22">2057489610.1080/10937404.2010.483933)</searchLink><br />Andersen ME, Krewski D (2009) Toxicity testing in the 21st century: bringing the vision to life. Toxicol Sci 107(2):324–330. (PMID: <searchLink fieldCode="PM" term="%221907476310%2E1093%2Ftoxsci%2Fkfn255%22">1907476310.1093/toxsci/kfn255)</searchLink><br />Andersen ME, Krewski D (2010) The vision of toxicity testing in the 21st century: moving from discussion to action. Toxicol Sci 117(1):17–24. (PMID: <searchLink fieldCode="PM" term="%222057378410%2E1093%2Ftoxsci%2Fkfq188%22">2057378410.1093/toxsci/kfq188)</searchLink><br />Testing CoT, Assessment of Environmental Agents NRC (2007) Toxicity testing in the 21st century: a vision and a strategy. The National Academies Press, Washington, DC.<br />Hendrickx DM, Boyles RR, Kleinjans JC et al (2014) Workshop report: identifying opportunities for global integration of toxicogenomics databases, 26-27 June 2013, Research Triangle Park, NC, USA. Arch Toxicol 88(12):2323–2332. (PMID: <searchLink fieldCode="PM" term="%2225326818424747810%2E1007%2Fs00204-014-1387-3%22">25326818424747810.1007/s00204-014-1387-3)</searchLink><br />Jacobs A (2009) An FDA perspective on the nonclinical use of the X-Omics technologies and the safety of new drugs. Toxicol Lett 186(1):32–35. (PMID: <searchLink fieldCode="PM" term="%221880947610%2E1016%2Fj%2Etoxlet%2E2008%2E08%2E013%22">1880947610.1016/j.toxlet.2008.08.013)</searchLink><br />Bhattacharya S, Zhang Q, Carmichael PL et al (2011) Toxicity testing in the 21 century: defining new risk assessment approaches based on perturbation of intracellular toxicity pathways. PLoS One 6(6):e20887. (PMID: <searchLink fieldCode="PM" term="%2221701582311880210%2E1371%2Fjournal%2Epone%2E0020887%22">21701582311880210.1371/journal.pone.0020887)</searchLink><br />Krewski D, Westphal M, Al-Zoughool M et al (2011) New directions in toxicity testing. Annu Rev Public Health 32:161–178. (PMID: <searchLink fieldCode="PM" term="%222121915410%2E1146%2Fannurev-publhealth-031210-101153%22">2121915410.1146/annurev-publhealth-031210-101153)</searchLink><br />Chepelev NL, Moffat ID, Labib S et al (2015) Integrating toxicogenomics into human health risk assessment: lessons learned from the benzo[a]pyrene case study. Crit Rev Toxicol 45(1):44–52. (PMID: <searchLink fieldCode="PM" term="%222560502710%2E3109%2F10408444%2E2014%2E973935%22">2560502710.3109/10408444.2014.973935)</searchLink><br />Moffat I, Chepelev N, Labib S et al (2015) Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water. Crit Rev Toxicol 45(1):1–43. (PMID: <searchLink fieldCode="PM" term="%2225605026452160810%2E3109%2F10408444%2E2014%2E973934%22">25605026452160810.3109/10408444.2014.973934)</searchLink><br />Harrill AH, Rusyn I (2008) Systems biology and functional genomics approaches for the identification of cellular responses to drug toxicity. Expert Opin Drug Metab Toxicol 4(11):1379–1389. (PMID: <searchLink fieldCode="PM" term="%2218950280261428410%2E1517%2F17425255%2E4%2E11%2E1379%22">18950280261428410.1517/17425255.4.11.1379)</searchLink><br />Zhang Q, Bhattacharya S, Andersen ME et al (2010) Computational systems biology and dose-response modeling in relation to new directions in toxicity testing. J Toxicol Environ Health B Crit Rev 13(2–4):253–276. (PMID: <searchLink fieldCode="PM" term="%222057490110%2E1080%2F10937404%2E2010%2E483943%22">2057490110.1080/10937404.2010.483943)</searchLink><br />Grant GR, Manduchi E, Stoeckert CJ Jr (2007) Analysis and management of microarray gene expression data [Chapter 19, unit 6]. Curr Protoc Mol Biol 77(1):1–30. (PMID: <searchLink fieldCode="PM" term="%2210%2E1002%2F0471142727%2Emb1906s77%22">10.1002/0471142727.mb1906s77)</searchLink><br />Gatzidou ET, Zira AN, Theocharis SE (2007) Toxicogenomics: a pivotal piece in the puzzle of toxicological research. J Appl Toxicol 27(4):302–309. (PMID: <searchLink fieldCode="PM" term="%221742980010%2E1002%2Fjat%2E1248%22">1742980010.1002/jat.1248)</searchLink><br />Jean-Quartier C, Jeanquartier F, Jurisica I et al (2018) In silico cancer research towards 3R. BMC Cancer 18(1):408. (PMID: <searchLink fieldCode="PM" term="%2229649981589793310%2E1186%2Fs12885-018-4302-0%22">29649981589793310.1186/s12885-018-4302-0)</searchLink><br />Vachon J, Page-Lariviere F, Sirard MA et al (2018) Availability, quality, and relevance of toxicogenomics data for human health risk assessment: a scoping review of the literature on trihalomethanes. Toxicol Sci 163(2):364–373. (PMID: <searchLink fieldCode="PM" term="%222951433210%2E1093%2Ftoxsci%2Fkfy050%22">2951433210.1093/toxsci/kfy050)</searchLink><br />Telenius H, Carter NP, Bebb CE et al (1992) Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13(3):718–725. (PMID: <searchLink fieldCode="PM" term="%22163939910%2E1016%2F0888-7543%2892%2990147-K%22">163939910.1016/0888-7543(92)90147-K)</searchLink><br />Zhang L, Cui X, Schmitt K et al (1992) Whole genome amplification from a single cell: implications for genetic analysis. Proc Natl Acad Sci USA 89(13):5847–5851. (PMID: <searchLink fieldCode="PM" term="%2216310674939410%2E1073%2Fpnas%2E89%2E13%2E5847%22">16310674939410.1073/pnas.89.13.5847)</searchLink><br />Huber R, Kulka U, Lorch T et al (2001) Technical report: application of the Metafer2 fluorescence scanning system for the analysis of radiation-induced chromosome aberrations measured by FISH-chromosome painting. Mutat Res 492(1–2):51–57. (PMID: <searchLink fieldCode="PM" term="%221137724310%2E1016%2FS1383-5718%2801%2900151-6%22">1137724310.1016/S1383-5718(01)00151-6)</searchLink><br />Bangs CD, Donlon TA (2005) Metaphase chromosome preparation from cultured peripheral blood cells. Curr Protoc Hum Genet Chapter 4:Unit 4.1. (PMID: <searchLink fieldCode="PM" term="%2218428376%22">18428376)</searchLink><br />du Manoir S, Kallioniemi OP, Lichter P et al (1995) Hardware and software requirements for quantitative analysis of comparative genomic hybridization. Cytometry 19(1):4–9. (PMID: <searchLink fieldCode="PM" term="%22770518310%2E1002%2Fcyto%2E990190103%22">770518310.1002/cyto.990190103)</searchLink><br />du Manoir S, Schrock E, Bentz M et al (1995) Quantitative analysis of comparative genomic hybridization. Cytometry 19(1):27–41. (PMID: <searchLink fieldCode="PM" term="%22770518210%2E1002%2Fcyto%2E990190105%22">770518210.1002/cyto.990190105)</searchLink><br />Lundsteen C, Maahr J, Christensen B et al (1995) Image analysis in comparative genomic hybridization. Cytometry 19(1):42–50. 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